STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [ChIP-seq]

Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. Here, we applied STARR-seq, a genome-wide plasmid-based assay, to measure the enhancer potential of genomic loci in a plasmid context in “ground-state” (2i+LIF; 2iL-ESCs) and “metastable” (serum+LIF; SL-ESCs) embryonic stem cells. Overall design: ZIC3 ChIP-seq of 2 biological replicates in mouse embryonic stem cells cultured in 2i+LIF or serum+LIF (4 samples total)

增强子（Enhancer）是基因表达的远端调控元件，能够塑造细胞身份并调控细胞命运转变。小鼠胚胎干细胞（mouse embryonic stem cells, mESCs）是一类典型细胞，其多能性身份由复杂的增强子图谱维持，且在分化过程中发生剧烈重塑。全基因组染色质开放度检测与组蛋白修饰实验通常被用作推断增强子位置、活性强度及动态变化的替代指标。本研究采用基于质粒的全基因组检测技术STARR-seq，在质粒环境中检测‘基础态’（2i+LIF；2iL-ESCs）与‘亚稳态’（血清+LIF；SL-ESCs）胚胎干细胞的基因组位点增强子潜能。实验整体设计：对培养于2i+LIF或血清+LIF条件下的小鼠胚胎干细胞，开展2次生物学重复的ZIC3染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing, ChIP-seq），总计4个样本。